A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data.

View Abstract

Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical power We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content. Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.

Investigators
Abbreviation
Epigenetics
Publication Date
2023-09-20
Volume
18
Issue
1
Page Numbers
2257437
Pubmed ID
37731367
Medium
Print-Electronic
Full Title
A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data.
Authors
Hecker J, Lee S, Kachroo P, Prokopenko D, Maaser-Hecker A, Lutz SM, Hahn G, Irizarry R, Weiss ST, DeMeo DL, Lange C